[med-svn] [libfreecontact-perl] 07/46: Imported Upstream version 0.01
Laszlo Kajan
lkajan at alioth.debian.org
Thu Sep 19 15:54:59 UTC 2013
This is an automated email from the git hooks/post-receive script.
lkajan pushed a commit to branch master
in repository libfreecontact-perl.
commit d7a93140c9ca85f49d5ec20a1fc9e31e75304e8f
Author: Laszlo Kajan <lkajan at debian.org>
Date: Fri May 10 18:41:07 2013 +0200
Imported Upstream version 0.01
---
FreeContact.c | 410 ---------------------------------------------------------
MANIFEST | 2 -
MANIFEST.SKIP | 4 +-
3 files changed, 2 insertions(+), 414 deletions(-)
diff --git a/FreeContact.bs b/FreeContact.bs
deleted file mode 100644
index e69de29..0000000
diff --git a/FreeContact.c b/FreeContact.c
deleted file mode 100644
index 086904e..0000000
--- a/FreeContact.c
+++ /dev/null
@@ -1,410 +0,0 @@
-/*
- * This file was generated automatically by ExtUtils::ParseXS version 2.2206 from the
- * contents of FreeContact.xs. Do not edit this file, edit FreeContact.xs instead.
- *
- * ANY CHANGES MADE HERE WILL BE LOST!
- *
- */
-
-#line 1 "FreeContact.xs"
-/* Copyright (C) 2013 by Laszlo Kajan, Technical University of Munich, Germany
-
- This program is free software; you can redistribute it and/or modify
- it under the same terms as Perl itself, either Perl version 5.10.1 or,
- at your option, any later version of Perl 5 you may have available.
-*/
-#include <freecontact.h>
-
-#ifdef __cplusplus
-extern "C" {
-#include "EXTERN.h"
-#include "perl.h"
-#include "XSUB.h"
-}
-#endif
-
-using namespace freecontact;
-typedef freecontact::predictor::cont_res_t cont_res_t;
-typedef freecontact::predictor::time_res_t time_res_t;
-
-#define _XPUSHS_GET_PS(__ps) \
- XPUSHs(sv_2mortal(newSVpvn("clustpc", 7)));\
- XPUSHs(sv_2mortal(newSVnv((__ps).clustpc)));\
- XPUSHs(sv_2mortal(newSVpvn("sparsity", 8)));\
- XPUSHs(sv_2mortal(newSVnv((__ps).sparsity)));\
- XPUSHs(sv_2mortal(newSVpvn("gapth", 5)));\
- XPUSHs(sv_2mortal(newSVnv((__ps).gapth)));\
- XPUSHs(sv_2mortal(newSVpvn("mincontsep", 10)));\
- XPUSHs(sv_2mortal(newSVuv((__ps).mincontsep)));\
-\
- XPUSHs(sv_2mortal(newSVpvn("pseudocnt", 9)));\
- XPUSHs(sv_2mortal(newSVnv((__ps).pseudocnt)));\
- XPUSHs(sv_2mortal(newSVpvn("pscnt_weight", 12)));\
- XPUSHs(sv_2mortal(newSVnv((__ps).pscnt_weight)));\
- XPUSHs(sv_2mortal(newSVpvn("estimate_ivcov", 14)));\
- XPUSHs(sv_2mortal(newSViv((__ps).estimate_ivcov)));\
- XPUSHs(sv_2mortal(newSVpvn("shrink_lambda", 13)));\
- XPUSHs(sv_2mortal(newSVnv((__ps).shrink_lambda)));\
-\
- XPUSHs(sv_2mortal(newSVpvn("cov20", 5)));\
- XPUSHs(sv_2mortal(newSViv((__ps).cov20)));\
- XPUSHs(sv_2mortal(newSVpvn("gap_incovm", 10)));\
- XPUSHs(sv_2mortal(newSViv((__ps).gap_incovm)));\
- XPUSHs(sv_2mortal(newSVpvn("veczw", 5)));\
- XPUSHs(sv_2mortal(newSViv((__ps).veczw)));\
- XPUSHs(sv_2mortal(newSVpvn("rho", 3)));\
- XPUSHs(sv_2mortal(newSVnv((__ps).rho)));
-
-#line 59 "FreeContact.c"
-#ifndef PERL_UNUSED_VAR
-# define PERL_UNUSED_VAR(var) if (0) var = var
-#endif
-
-#ifndef PERL_ARGS_ASSERT_CROAK_XS_USAGE
-#define PERL_ARGS_ASSERT_CROAK_XS_USAGE assert(cv); assert(params)
-
-/* prototype to pass -Wmissing-prototypes */
-STATIC void
-S_croak_xs_usage(pTHX_ const CV *const cv, const char *const params);
-
-STATIC void
-S_croak_xs_usage(pTHX_ const CV *const cv, const char *const params)
-{
- const GV *const gv = CvGV(cv);
-
- PERL_ARGS_ASSERT_CROAK_XS_USAGE;
-
- if (gv) {
- const char *const gvname = GvNAME(gv);
- const HV *const stash = GvSTASH(gv);
- const char *const hvname = stash ? HvNAME(stash) : NULL;
-
- if (hvname)
- Perl_croak(aTHX_ "Usage: %s::%s(%s)", hvname, gvname, params);
- else
- Perl_croak(aTHX_ "Usage: %s(%s)", gvname, params);
- } else {
- /* Pants. I don't think that it should be possible to get here. */
- Perl_croak(aTHX_ "Usage: CODE(0x%"UVxf")(%s)", PTR2UV(cv), params);
- }
-}
-#undef PERL_ARGS_ASSERT_CROAK_XS_USAGE
-
-#ifdef PERL_IMPLICIT_CONTEXT
-#define croak_xs_usage(a,b) S_croak_xs_usage(aTHX_ a,b)
-#else
-#define croak_xs_usage S_croak_xs_usage
-#endif
-
-#endif
-
-/* NOTE: the prototype of newXSproto() is different in versions of perls,
- * so we define a portable version of newXSproto()
- */
-#ifdef newXS_flags
-#define newXSproto_portable(name, c_impl, file, proto) newXS_flags(name, c_impl, file, proto, 0)
-#else
-#define newXSproto_portable(name, c_impl, file, proto) (PL_Sv=(SV*)newXS(name, c_impl, file), sv_setpv(PL_Sv, proto), (CV*)PL_Sv)
-#endif /* !defined(newXS_flags) */
-
-#line 111 "FreeContact.c"
-
-/* INCLUDE_COMMAND: Including output of '/usr/bin/perl -MExtUtils::XSpp::Cmd -e xspp -- --typemap=typemap.xsp FreeContact.xsp' from 'FreeContact.xs' */
-
-#include <exception>
-
-
-XS(XS_FreeContact_get_ps_evfold); /* prototype to pass -Wmissing-prototypes */
-XS(XS_FreeContact_get_ps_evfold)
-{
-#ifdef dVAR
- dVAR; dXSARGS;
-#else
- dXSARGS;
-#endif
- if (items != 0)
- croak_xs_usage(cv, "");
- PERL_UNUSED_VAR(ax); /* -Wall */
- SP -= items;
- {
-#line 12 "/usr/bin/perl -MExtUtils::XSpp::Cmd -e xspp -- --typemap=typemap.xsp FreeContact.xsp"
- _XPUSHS_GET_PS(ps_evfold);
-#line 133 "FreeContact.c"
- PUTBACK;
- return;
- }
-}
-
-
-XS(XS_FreeContact_get_ps_psicov); /* prototype to pass -Wmissing-prototypes */
-XS(XS_FreeContact_get_ps_psicov)
-{
-#ifdef dVAR
- dVAR; dXSARGS;
-#else
- dXSARGS;
-#endif
- if (items != 0)
- croak_xs_usage(cv, "");
- PERL_UNUSED_VAR(ax); /* -Wall */
- SP -= items;
- {
-#line 17 "/usr/bin/perl -MExtUtils::XSpp::Cmd -e xspp -- --typemap=typemap.xsp FreeContact.xsp"
- _XPUSHS_GET_PS(ps_psicov);
-#line 155 "FreeContact.c"
- PUTBACK;
- return;
- }
-}
-
-
-XS(XS_FreeContact__Predictor_new); /* prototype to pass -Wmissing-prototypes */
-XS(XS_FreeContact__Predictor_new)
-{
-#ifdef dVAR
- dVAR; dXSARGS;
-#else
- dXSARGS;
-#endif
- if (items < 1 || items > 2)
- croak_xs_usage(cv, "CLASS, __dbg = false");
- {
- bool __dbg;
- char * CLASS = (char *)SvPV_nolen(ST(0));
- predictor * RETVAL;
-
- if (items < 2)
- __dbg = false;
- else {
- __dbg = (bool)SvTRUE(ST(1));
- }
-#line 28 "/usr/bin/perl -MExtUtils::XSpp::Cmd -e xspp -- --typemap=typemap.xsp FreeContact.xsp"
- try {
- RETVAL = new predictor( __dbg );
- }
- catch (std::exception& e) {
- croak("Caught C++ exception of type or derived from 'std::exception': %s", e.what());
- }
- catch (...) {
- croak("Caught C++ exception of unknown type");
- }
-#line 192 "FreeContact.c"
- ST(0) = sv_newmortal();
- sv_setref_pv( ST(0), CLASS, (void*)RETVAL );
-
- }
- XSRETURN(1);
-}
-
-
-XS(XS_FreeContact__Predictor_DESTROY); /* prototype to pass -Wmissing-prototypes */
-XS(XS_FreeContact__Predictor_DESTROY)
-{
-#ifdef dVAR
- dVAR; dXSARGS;
-#else
- dXSARGS;
-#endif
- if (items != 1)
- croak_xs_usage(cv, "THIS");
- {
- predictor * THIS;
-
- if( sv_isobject(ST(0)) && (SvTYPE(SvRV(ST(0))) == SVt_PVMG) )
- THIS = (predictor *)SvIV((SV*)SvRV( ST(0) ));
- else{
- warn( "FreeContact::Predictor::DESTROY() -- THIS is not a blessed SV reference" );
- XSRETURN_UNDEF;
- };
-#line 42 "/usr/bin/perl -MExtUtils::XSpp::Cmd -e xspp -- --typemap=typemap.xsp FreeContact.xsp"
- try {
- delete THIS;
- }
- catch (std::exception& e) {
- croak("Caught C++ exception of type or derived from 'std::exception': %s", e.what());
- }
- catch (...) {
- croak("Caught C++ exception of unknown type");
- }
-#line 230 "FreeContact.c"
- }
- XSRETURN_EMPTY;
-}
-
-
-XS(XS_FreeContact__Predictor__run); /* prototype to pass -Wmissing-prototypes */
-XS(XS_FreeContact__Predictor__run)
-{
-#ifdef dVAR
- dVAR; dXSARGS;
-#else
- dXSARGS;
-#endif
- if (items < 14 || items > 16)
- croak_xs_usage(cv, "THIS, __ali, __cp, __spar, __gapth, __mincontsep, __pseudocnt, __pscnt_weight, __estimate_ivcov, __shrink_lambda, __cov20, __gap_incovm, __vecw, __rho, __num_threads = 0, __timing = NULL");
- {
- ali_t __ali;
- double __cp = (double)SvNV(ST(2));
- double __spar = (double)SvNV(ST(3));
- double __gapth = (double)SvNV(ST(4));
- U16 __mincontsep = (unsigned short)SvUV(ST(5));
- double __pseudocnt = (double)SvNV(ST(6));
- double __pscnt_weight = (double)SvNV(ST(7));
- bool __estimate_ivcov = (bool)SvTRUE(ST(8));
- double __shrink_lambda = (double)SvNV(ST(9));
- bool __cov20 = (bool)SvTRUE(ST(10));
- bool __gap_incovm = (bool)SvTRUE(ST(11));
- bool __vecw = (bool)SvTRUE(ST(12));
- double __rho = (double)SvNV(ST(13));
- int __num_threads;
- time_res_t* __timing;
-#line 73 "/usr/bin/perl -MExtUtils::XSpp::Cmd -e xspp -- --typemap=typemap.xsp FreeContact.xsp"
- time_res_t timing;
-#line 264 "FreeContact.c"
- predictor * THIS;
- cont_res_t RETVAL;
-
- {
- if(SvROK(ST(1)) && SvTYPE(SvRV(ST(1))) == SVt_PVAV)
- {
- // ST(1) is an array reference to strings - the sequences in the alignment
- AV *arr = (AV*)SvRV(ST(1));
- I32 seqcnt = av_len(arr)+1; // av_len returns highest index
- if(seqcnt > 0)
- {
- SV** lineptr = av_fetch(arr, 0, false);
- if(lineptr != NULL && SvPOK(*lineptr))
- {
- STRLEN alilen = SvCUR(*lineptr);
- if(alilen <= 0xFFFF)
- {
- __ali = ali_t(alilen);
-
- for(I32 k = 0; k < seqcnt; ++k)
- {
- SV** lineptr = av_fetch(arr, k, false);
- if(lineptr != NULL && SvPOK(*lineptr))
- {
- STRLEN alilen = SvCUR(*lineptr);
- if(alilen <= 0xFFFF)
- {
- const char *al = SvPVbyte(*lineptr, alilen);
- __ali.push(std::string(al, alilen));
- }
- }
- }
- }
- else croak("FreeContact::Predictor::_run() -- __ali->[0] is too long");
- }
- else croak("FreeContact::Predictor::_run() -- __ali->[0] is not a character string");
- }
- }
- else croak("FreeContact::Predictor::_run() -- __ali is not an AV reference");
- };
-
- if (items < 15)
- __num_threads = 0;
- else {
- __num_threads = (int)SvIV(ST(14));
- }
-
- if (items < 16)
- __timing = NULL;
- else {
- __timing = (time_res_t*)~NULL;
- }
-
- if( sv_isobject(ST(0)) && (SvTYPE(SvRV(ST(0))) == SVt_PVMG) )
- THIS = (predictor *)SvIV((SV*)SvRV( ST(0) ));
- else{
- warn( "FreeContact::Predictor::_run() -- THIS is not a blessed SV reference" );
- XSRETURN_UNDEF;
- };
-#line 75 "/usr/bin/perl -MExtUtils::XSpp::Cmd -e xspp -- --typemap=typemap.xsp FreeContact.xsp"
- try {
- if(__timing) __timing = &timing;
- RETVAL = THIS->run( __ali, __cp, __spar, __gapth, __mincontsep, __pseudocnt, __pscnt_weight, __estimate_ivcov, __shrink_lambda, __cov20, __gap_incovm, __vecw, __rho, __num_threads, __timing );
- }
- catch (std::exception& e) {
- croak("Caught C++ exception of type or derived from 'std::exception': %s", e.what());
- }
- catch (...) {
- croak("Caught C++ exception of unknown type");
- }
-#line 335 "FreeContact.c"
- if(__timing && SvROK(ST(15)) && SvTYPE(SvRV(ST(15))) == SVt_PVHV)
- {
- // return { 'key' => 0.0, ... }
- HV* res = (HV*)SvRV(ST(15));
- for(time_res_t::const_iterator tr_i = __timing->begin(), tr_e = __timing->end(); tr_i != tr_e; ++tr_i)
- hv_store(res, tr_i->first.c_str(), tr_i->first.length(), newSVnv(tr_i->second), 0);
- }
-
- SvSETMAGIC(ST(15));
- ST(0) = sv_newmortal();
- if(RETVAL.empty()) ST(0) = &PL_sv_undef;
- else
- {
-
- // return { 'l1norm' => [ [ 0, 1, 45.786 ], [ 0, 2, 7.993 ], ... ], ... }
- HV* res = (HV*)sv_2mortal((SV*)newHV());
- for(cont_res_t::const_iterator cr_i = RETVAL.begin(), cr_e = RETVAL.end(); cr_i != cr_e; ++cr_i)
- {
- AV* contacts = (AV*)sv_2mortal((SV*)newAV()); av_extend(contacts, cr_i->second.size()-1); // extend to index
-
- for(std::vector<contact_t>::const_iterator ct_i = cr_i->second.begin(), ct_e = cr_i->second.end(); ct_i != ct_e; ++ct_i)
- {
- AV* ijscore = (AV*)sv_2mortal((SV*)newAV()); av_extend(ijscore, 2); // extend to index
-
- av_push(ijscore, newSVuv(ct_i->i));
- av_push(ijscore, newSVuv(ct_i->j));
- av_push(ijscore, newSVnv(ct_i->score));
- //
- av_push(contacts, newRV((SV*)ijscore));
- }
-
- hv_store(res, cr_i->first.c_str(), cr_i->first.length(), newRV((SV*)contacts), 0);
- }
-
- sv_setsv(ST(0), newRV((SV*)res));
- }
- }
- XSRETURN(1);
-}
-
-
-/* INCLUDE: Returning to 'FreeContact.xs' from '/usr/bin/perl -MExtUtils::XSpp::Cmd -e xspp -- --typemap=typemap.xsp FreeContact.xsp' */
-
-#ifdef __cplusplus
-extern "C"
-#endif
-XS(boot_FreeContact); /* prototype to pass -Wmissing-prototypes */
-XS(boot_FreeContact)
-{
-#ifdef dVAR
- dVAR; dXSARGS;
-#else
- dXSARGS;
-#endif
-#if (PERL_REVISION == 5 && PERL_VERSION < 9)
- char* file = __FILE__;
-#else
- const char* file = __FILE__;
-#endif
-
- PERL_UNUSED_VAR(cv); /* -W */
- PERL_UNUSED_VAR(items); /* -W */
- XS_VERSION_BOOTCHECK ;
-
- newXS("FreeContact::get_ps_evfold", XS_FreeContact_get_ps_evfold, file);
- newXS("FreeContact::get_ps_psicov", XS_FreeContact_get_ps_psicov, file);
- newXS("FreeContact::Predictor::new", XS_FreeContact__Predictor_new, file);
- newXS("FreeContact::Predictor::DESTROY", XS_FreeContact__Predictor_DESTROY, file);
- newXS("FreeContact::Predictor::_run", XS_FreeContact__Predictor__run, file);
-#if (PERL_REVISION == 5 && PERL_VERSION >= 9)
- if (PL_unitcheckav)
- call_list(PL_scopestack_ix, PL_unitcheckav);
-#endif
- XSRETURN_YES;
-}
-
diff --git a/MANIFEST b/MANIFEST
index 408dd5d..eedeae9 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -1,7 +1,5 @@
Changes
examples/demo_1000.aln
-FreeContact.bs
-FreeContact.c
FreeContact.xs
FreeContact.xsp
lib/FreeContact.pm
diff --git a/MANIFEST.SKIP b/MANIFEST.SKIP
index 0c34b60..0e81c31 100644
--- a/MANIFEST.SKIP
+++ b/MANIFEST.SKIP
@@ -23,6 +23,8 @@
\b_build/
\.o$
\.tar\.gz$
+FreeContact.bs
+FreeContact.c
# Avoid temp and backup files.
~$
@@ -37,5 +39,3 @@
.swp$
.vim$
-debian
-zergtest
--
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